General information for g12828.t7
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g12828 is located on chr_1: 26451910..26454473 (+ strand)
Gene structure
- The exon-intron structure of all isoforms are indicated below. CDS regions are colored in green. TSS and TTs that were predicted with CTR-Seq data are indicated in solid circle and squares, respectively. More specific data are shown in the table below.
| Chromosome | Gene | Transcript | Category | ID | Start | End |
|---|---|---|---|---|---|---|
| chr_1 | g12828 | g12828.t7 | TSS | g12828.t7 | 26451765 | 26451765 |
| chr_1 | g12828 | g12828.t7 | isoform | g12828.t7 | 26451910 | 26452726 |
| chr_1 | g12828 | g12828.t7 | exon | g12828.t7.exon1 | 26451910 | 26452282 |
| chr_1 | g12828 | g12828.t7 | cds | g12828.t7.CDS1 | 26452105 | 26452282 |
| chr_1 | g12828 | g12828.t7 | exon | g12828.t7.exon2 | 26452339 | 26452726 |
| chr_1 | g12828 | g12828.t7 | cds | g12828.t7.CDS2 | 26452339 | 26452724 |
| chr_1 | g12828 | g12828.t7 | TTS | g12828.t7 | NA | NA |
Sequences
>g12828.t7 Gene=g12828 Length=761
ATGTCTGTTGCCTATTCATCAAGTCAAAATCCGGCAACAAATCAGCAGCCGAGACCAAAT
GTTCCTCCACAACCGCAAAGGTATAATAAATACATGAATGCTGTTGAATTTTTTAAAATA
TTTAAATTTTTCTCTTAATAATTAATCAAAAATAGACCAACTGGACCACCACCGAATCCT
GCTCAAATACAGAAAATGCTCGATGAAAATTGCAGTCTTATTCAAACTATTCAAGATTAT
CAGAATATGGGAAAAGCTAATGAATGCATTTCTCATCAACAAGCATTACATAGAAATCTT
CTTTATCTTGCATCATTAGCAGATTCAACACAAAATATGTCACAATTATTGCCTGTAAGT
TTTCTTTTAAAAACACAAGGTGGACCAATTCCTCCTCCAATGATGAATGAACCGTCTCAG
CCGAATTACAATGCTCCCATGCAACAACCTGGTATGCAAATGGGAAATCAACCGATTCCA
TCGCCTCAACAAATGCCAATGCAAATGCCTCCACAACAAAATACAACTGTTAATCCACAA
ATGCCGCCAACTTCTCAAGCAGCTGTTCCGAATCCGAATCAACCTTATAGAGTTCAAACA
CCAAGTTCACAACAACCTCCAGTTTCAGCACAAAATCAACCACCCGTTACATCTCAAGCA
CAAATTAATTCTCCACAGCCAACAACACAAACACAACAGCAACCTGCTCAAAATCCTCGT
GCTGCAAACACACCTCAAACAAACCCAATAACGAACCCAGC
>g12828.t7 Gene=g12828 Length=188
MLDENCSLIQTIQDYQNMGKANECISHQQALHRNLLYLASLADSTQNMSQLLPVSFLLKT
QGGPIPPPMMNEPSQPNYNAPMQQPGMQMGNQPIPSPQQMPMQMPPQQNTTVNPQMPPTS
QAAVPNPNQPYRVQTPSSQQPPVSAQNQPPVTSQAQINSPQPTTQTQQQPAQNPRAANTP
QTNPITNP
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 3 | g12828.t7 | MobiDBLite | mobidb-lite | consensus disorder prediction | 89 | 119 | - |
| 5 | g12828.t7 | MobiDBLite | mobidb-lite | consensus disorder prediction | 89 | 188 | - |
| 4 | g12828.t7 | MobiDBLite | mobidb-lite | consensus disorder prediction | 125 | 188 | - |
| 2 | g12828.t7 | PANTHER | PTHR23107 | SYNOVIAL SARCOMA ASSOCIATED SS18 PROTEIN | 1 | 183 | 8.4E-19 |
| 1 | g12828.t7 | Pfam | PF05030 | SSXT protein (N-terminal region) | 1 | 50 | 7.6E-24 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0003713 | transcription coactivator activity | MF |
KEGG
Orthology
This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).
Expression
Transcript expression in Pv11 cells
TPM values are indicated as average +/- STDEV. 
Differential expression
Differentially expressed genes were identified with DESeq2 using the ‘run_DE_analysis.pl’ script from Trinity. Transcripts were determined as differentially expressed when (1) FDR < 0.05 (2) fold change > 2 (TPM calculated by RSEM). DE information and fold change between conditions are indicated in the plot below. There were no conditions that were differentially expressed